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- EMDB-52720: Human gamma-tubulin ring complex from purified centrosomes of CDK... -

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Basic information

Entry
Database: EMDB / ID: EMD-52720
TitleHuman gamma-tubulin ring complex from purified centrosomes of CDK5RAP2-knockout cells
Map dataSubtomogram average of human gamma-TuRC purified from CDK5RAP2 knockout centrosomes
Sample
  • Complex: gamma-tubulin ring complex from purified human centrosomes
Keywordscentrosome / cytoskeleton / microtubule / microtubule nucleation / complex / template / cap / gamma-tubulin / gamma-tubulin ring complex / cell cycle / nedd1 / neural precursor cell-expressed developmentally down-regulated 1 / CDK5RAP2 / cyclin-dependent kinase 5 regulatory subunit associated protein 2
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 31.0 Å
AuthorsHofer FW / Pfeffer S
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG Schi 295/4-4 Germany
German Research Foundation (DFG)DFG SCHI 295/11-1 Germany
German Research Foundation (DFG)DFG PF 963/1-4 Germany
German Research Foundation (DFG)DFG PF 963/4-1 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural mechanisms for centrosomal recruitment and organization of the microtubule nucleator γ-TuRC.
Authors: Qi Gao / Florian W Hofer / Sebastian Filbeck / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Charlotte Kaplan / Maja Zezlina / Cornelia Sala / Hyesu Shin / Oliver J Gruss / Elmar ...Authors: Qi Gao / Florian W Hofer / Sebastian Filbeck / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Charlotte Kaplan / Maja Zezlina / Cornelia Sala / Hyesu Shin / Oliver J Gruss / Elmar Schiebel / Stefan Pfeffer /
Abstract: The γ-tubulin ring complex (γ-TuRC) acts as a structural template for microtubule formation at centrosomes, associating with two main compartments: the pericentriolar material and the centriole ...The γ-tubulin ring complex (γ-TuRC) acts as a structural template for microtubule formation at centrosomes, associating with two main compartments: the pericentriolar material and the centriole lumen. In the pericentriolar material, the γ-TuRC is involved in microtubule organization, while the function of the centriole lumenal pool remains unclear. The conformational landscape of the γ-TuRC, which is crucial for its activity, and its centrosomal anchoring mechanisms, which determine γ-TuRC activity and turnover, are not understood. Using cryo-electron tomography, we analyze γ-TuRCs in human cells and purified centrosomes. Pericentriolar γ-TuRCs simultaneously associate with the essential adapter NEDD1 and the microcephaly protein CDK5RAP2. NEDD1 forms a tetrameric structure at the γ-TuRC base through interactions with four GCP3/MZT1 modules and GCP5/6-specific extensions, while multiple copies of CDK5RAP2 engage the γ-TuRC in two distinct binding patterns to promote γ-TuRC closure and activation. In the centriole lumen, the microtubule branching factor Augmin tethers a condensed cluster of γ-TuRCs to the centriole wall with defined directional orientation. Centriole-lumenal γ-TuRC-Augmin is protected from degradation during interphase and released in mitosis to aid chromosome alignment. This study provides a unique view on γ-TuRC structure and molecular organization at centrosomes and identifies an important cellular function of centriole-lumenal γ-TuRCs.
History
DepositionFeb 4, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52720.png

Downloads & links

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Map

FileDownload / File: emd_52720.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of human gamma-TuRC purified from CDK5RAP2 knockout centrosomes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.08 Å/pix.
x 128 pix.
= 650.24 Å		5.08 Å/pix.
x 128 pix.
= 650.24 Å		5.08 Å/pix.
x 128 pix.
= 650.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.514
Minimum - Maximum-0.34912986 - 1.2061659
Average (Standard dev.)0.0062536225 (±0.09560104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 650.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map for subtomogram average of human gamma-TuRC...

Fileemd_52720_half_map_1.map
AnnotationHalf map for subtomogram average of human gamma-TuRC purified from CDK5RAP2 knockout centrosomes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for subtomogram average of human gamma-TuRC...

Fileemd_52720_half_map_2.map
AnnotationHalf map for subtomogram average of human gamma-TuRC purified from CDK5RAP2 knockout centrosomes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : gamma-tubulin ring complex from purified human centrosomes

EntireName: gamma-tubulin ring complex from purified human centrosomes
Components
  • Complex: gamma-tubulin ring complex from purified human centrosomes

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Supramolecule #1: gamma-tubulin ring complex from purified human centrosomes

SupramoleculeName: gamma-tubulin ring complex from purified human centrosomes
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Organelle: Centrosome

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
Component:
ConcentrationName
10.0 mMPipes
0.1 %Triton X-100
0.1 %beta-mercaptoethanol
60.0 %sucrose
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 5.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 2848
ExtractionNumber tomograms: 21 / Number images used: 25014 / Software: (Name: PyTom (ver. 0.971), Warp (ver. 1.09))
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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